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10 Active Transport of ATP, ADP, and Pi Across the Mitochondrial Membrane
GLOSSARY OF BIOCHEMICAL TERMS
elongation factor. A protein that is involved
in extending the peptide chain during protein synthesis.
enantiomers. Stereoisomers that are nonsuperimposable mirror images.
endocytosis. The process by which matter is
engulfed by a plasma membrane and brought
into the cell within a lipid vesicle derived
from the membrane.
endonuclease. An enzyme that catalyzes the
hydrolysis of phosphodiester linkages at various sites within polynucleotide chains.
endoplasmic reticulum. A membranous
network of tubules and sheets continuous
with the outer nuclear membrane of eukaryotic cells. Regions of the endoplasmic reticulum coated with ribosomes are called the
rough endoplasmic reticulum; regions having no attached ribosomes are known as the
smooth endoplasmic reticulum. The endoplasmic reticulum is involved in the sorting
and transport of certain proteins and in the
synthesis of lipids.
endosomes. Smooth vesicles inside the cell
that are receptacles for endocytosed material.
energy-rich compound. A compound whose
hydrolysis occurs with a large negative freeenergy change (equal to or greater than that
for ATP : ADP + Pi).
enthalpy (H). A thermodynamic state function that describes the heat content of a system.
entropy (S). A thermodynamic state function that describes the randomness or disorder of a system.
enzymatic reaction. A reaction catalyzed by
a biological catalyst, an enzyme. Enzymatic
reactions are 103 to 1017 times faster than the
corresponding uncatalyzed reactions.
enzyme. A biological catalyst, almost always
a protein. Some enzymes may require additional cofactors for activity. Virtually all biochemical reactions are catalyzed by specific
enzyme assay. A method used to analyze the
activity of a sample of an enzyme. Typically,
enzymatic activity is measured under selected
conditions such that the rate of conversion of
substrate to product is proportional to enzyme concentration.
enzyme inhibitor. A compound that binds
to an enzyme and interferes with its activity
by preventing either the formation of the ES
complex or its conversion to E + P.
enzyme-substrate complex (ES). A complex
formed when substrate molecules bind noncovalently within the active site of an
epimers. Isomers that differ in configuration
at only one of several chiral centers.
equilibrium. The state of a system in which
the rate of conversion of substrate to product
is equal to the rate of conversion of product
to substrate. The free-energy change for a reaction or system at equilibrium is zero.
equilibrium constant (Keq). The ratio of the
concentrations of products to the concentrations of reactants at equilibrium. The equilibrium constant is related to the standard
Gibbs free energy change of reaction.
essential amino acid. An amino acid that
cannot be synthesized by an animal and must
be obtained in the diet.
essential fatty acid. A fatty acid that cannot
be synthesized by an animal and must be obtained in the diet.
essential ion. An ion required as a cofactor
for the catalytic activity of certain enzymes.
Some essential ions, called activator ions, are
reversibly bound to enzymes and often participate in the binding of substrates, whereas
tightly bound metal ions frequently participate directly in catalytic reactions.
eukaryote. An organism whose cells generally possess a nucleus and internal membranes (cf., prokaryote).
excision repair. The reversal of DNA damage by excision-repair endonucleases. Gross
lesions that alter the structure of the DNA
helix are repaired by cleavage on each side of
the lesion and removal of the damaged DNA.
The resulting single-stranded gap is filled by
DNA polymerase and sealed by DNA ligase.
exocytosis. The process by which material
destined for secretion from a cell is enclosed
in lipid vesicles that are transported to and
fuse with the plasma membrane, releasing
the material into the extracellular space.
exon. A nucleotide sequence that is present
in the primary RNA transcript and in the
mature RNA molecule. The term exon also
refers to the region of the gene that corresponds to a sequence present in the mature
RNA (cf., intron).
exonuclease. An enzyme that catalyzes the
sequential hydrolysis of phosphodiester linkages from one end of a polynucleotide chain.
extrinsic membrane protein. See peripheral
facilitated diffusion. See passive transport.
facultative anaerobe. An organism that can
survive in the presence or absence of oxygen.
fatty acid. A long chain aliphatic hydrocarbon with a single carboxyl group at one end.
Fatty acids are the simplest type of lipid and
are components of many more complex
lipids, including triacylglycerols, glycerophospholipids, sphingolipids, and waxes.
feedback inhibition. Inhibition of an enzyme that catalyzes an early step in a metabolic pathway by an end product of the same
feed-forward activation. Activation of an
enzyme in a metabolic pathway by a metabolite produced earlier in the pathway.
fermentation. The anaerobic catabolism of
metabolites for energy production. In alcoholic fermentation, pyruvate is converted to
ethanol and carbon dioxide.
fibrous proteins. A major class of water-insoluble proteins that associate to form long
fibers. Many fibrous proteins are physically
tough and provide mechanical support to individual cells or entire organisms.
first-order reaction. A reaction whose rate
is directly proportional to the concentration
of only one reactant.
Fischer projection. A two-dimensional representation of the three-dimensional structures of sugars and related compounds. In a
Fischer projection, the carbon skeleton is
drawn vertically, with C-1 at the top. At a chiral center, horizontal bonds extend toward
the viewer and vertical bonds extend away
from the viewer.
fluid mosaic model. A model proposed for
the structure of biological membranes. In
this model, the membrane is depicted as a dynamic structure in which lipids and membrane proteins (both integral and peripheral)
rotate and undergo lateral diffusion.
fluorescence. A form of luminescence in
which visible radiation is emitted from a
molecule as it passes from a higher to a lower
flux. The flow of material through a metabolic pathway. Flux depends on the supply of
substrates, the removal of products, and the
catalytic capabilities of the enzymes involved
in the pathway.
fold. A combination of secondary structures
that form the core of a protein domain. Many
different folds have been characterized.
frameshift mutation. An alteration in DNA
caused by the insertion or deletion of a number of nucleotides not divisible by three. A
frameshift mutation changes the reading
frame of the corresponding mRNA molecule
and affects translation of all codons downstream of the mutation.
free energy change. See Gibbs free energy
free radical. A molecule or atom with an
furanose. A monosaccharide structure that
forms a five-membered ring as a result of intramolecular hemiacetal formation.
G protein. A protein that binds guanine nucleotides.
≤G. See Gibbs free energy change.
≤G° œ . See standard Gibbs free energy change.
ganglioside. A glycosphingolipid in which
oligosaccharide chains containing N-acetylneuraminic acid are attached to a ceramide.
Gangliosides are present on cell surfaces and
provide cells with distinguishing surface
markers that may serve in cellular recognition and cell-to-cell communication.
gas chromatography. A chromatographic
technique used to separate components of a
mixture based on their partitioning between
the gas phase and a stationary phase, which
can be a liquid or solid.
GLOSSARY OF BIOCHEMICAL TERMS
gel-filtration chromatography. A chromatographic technique used to separate a mixture
of proteins or other macromolecules in solution based on molecular size, using a matrix of
porous beads. Also known as molecular-exclusion chromatography.
gene. Loosely defined as a segment of DNA
that is transcribed. In some cases, the term
gene may also be used to refer to a segment of
DNA that encodes a functional protein or
corresponds to a mature RNA molecule.
genetic code. The correspondence between
a particular three nucleotide codon and the
amino acid it specifies. The standard genetic
code of 64 codons is used by almost all organisms. The genetic code is used to translate
the sequence of nucleotides in mRNA into
genetic recombination. The exchange or
transfer of DNA from one molecule of DNA
to another (cf., homologous recombination).
genome. One complete set of the genetic information in an organism. It may be a single
chromosome or a set of chromosomes (haploid). Mitochondria and chloroplasts have
genomes separate from that in the nucleus of
Gibbs free energy change (≤G). A thermodynamic quantity that defines the equilibrium condition in terms of the changes in
enthalpy (H) and entropy (S) of a system at
constant pressure. ¢G = ¢H - T¢S, where
T is absolute temperature. Free energy is a
measure of the energy available within a system to do work.
globular proteins. A major class of proteins,
many of which are water soluble. Globular
proteins are compact and roughly spherical,
containing tightly folded polypeptide chains.
Typically, globular proteins include indentations, or clefts that specifically recognize and
transiently bind other compounds.
glucogenic compound. A compound, such
as an amino acid, that can be used for gluconeogenesis in animals.
gluconeogenesis. A pathway for synthesis of
glucose from a noncarbohydrate precursor.
Gluconeogenesis from pyruvate involves the
seven near-equilibrium reactions of glycolysis traversed in the reverse direction. The
three metabolically irreversible reactions of
glycolysis are bypassed by four enzymatic reactions that do not occur in glycolysis.
glucoside. A glycoside where the anomeric
carbon atom is from glucose.
glycan. A general term for an oligosaccharide
or a polysaccharide. A homoglycan is a polymer of identical monosaccharide residues; a
heteroglycan is a polymer of different monosaccharide residues.
glycerophospholipid. A lipid consisting of
two fatty acyl groups bound to C-1 and C-2 of
glycerol 3-phosphate and, in most cases, a
polar substituent attached to the phosphate
moiety. Glycerophospholipids are major components of biological membranes.
glycoconjugate. A carbohydrate derivative
in which one or more carbohydrate chains
are covalently linked to a peptide chain, protein, or lipid.
glycoforms. Glycoproteins containing identical amino acid sequences but different
glycogen. A branched homopolymer of glucose residues joined by a-(1 : 4) linkages
with a-(1 : 6) linkages at branch points.
Glycogen is a storage polysaccharide in animals and bacteria.
glycolysis. A catabolic pathway consisting of
10 enzyme-catalyzed reactions by which one
molecule of glucose is converted to two molecules of pyruvate. In the process, two molecules
of ATP are formed from ADP + Pi, and two
molecules of NAD1 are reduced to NADH.
glycoprotein. A protein that contains covalently bound carbohydrate residues.
glycosaminoglycan. An unbranched polysaccharide of repeating disaccharide units.
One component of the disaccharide is an
amino sugar; the other component is usually
a uronic acid.
glycoside. A molecule containing a carbohydrate in which the hydroxyl group of the
anomeric carbon has been replaced through
condensation with an alcohol, an amine, or a
glycosidic bond. Acetal linkage formed by
condensation of the anomeric carbon atom
of a saccharide with a hydroxyl, amino, or
thiol group of another molecule. The most
commonly encountered glycosidic bonds are
formed between the anomeric carbon of one
sugar and a hydroxyl group of another sugar.
Nucleosidic bonds are N-linked glycosidic
sphingosine and carbohydrate moieties.
glycosylation. See protein glycosylation.
glyoxylate cycle. A variation of the citric
acid cycle in certain plants, bacteria, and
yeast that allows net production of glucose
from acetyl CoA via oxaloacetate. The glyoxylate cycle bypasses the two CO22 producing steps of the citric acid cycle.
glyoxysome. An organelle that contains specialized enzymes for the glyoxylate cycle.
Golgi apparatus. A complex of flattened,
fluid-filled membranous sacs in eukaryotic
cells, often found in proximity to the endoplasmic reticulum. The Golgi apparatus is
involved in the modification, sorting, and
targeting of proteins.
granum. A stack of flattened vesicles formed
from the thylakoid membrane in chloroplasts.
group transfer potential. See photsphoryl
group transfer potential.
group transfer reaction. A reaction in
which a substituent or functional group is
transferred from one substrate to another.
H. See enthalpy.
hairpin. 1. A secondary structure adopted by
single-stranded polynucleotides that arises
when short regions fold back on themselves
and hydrogen bonds form between complementary bases. Also known as a stem-loop.
2. A tight turn connecting two consecutive
b strands of a polypeptide.
haploid. Having one set of chromosomes or
one copy of the genome (cf., diploid).
high energy molecule. See energy-rich
Haworth projection. A representation in
which a cyclic sugar molecule is depicted as a
flat ring that is projected perpendicular to the
plane of the page. Heavy lines represent the
part of the molecule that extends toward the
HDL. See high density lipoprotein.
heat of vaporization. The amount of heat
required to evaporate 1 gram of a liquid.
heat shock protein. A protein whose synthesis is increased in response to stresses such as
high temperature. Many heat shock proteins
are chaperones that are also expressed in the
absence of stress.
helicase. An enzyme that is involved in unwinding DNA.
hemiacetal. The product formed when an
alcohol reacts with an aldehyde.
hemiketal. The product formed when an alcohol reacts with a ketone.
Henderson-Hasselbalch equation. An equation that describes the pH of a solution of a
weak acid or a weak base in terms of the pKa
and the concentrations of the proton donor
and proton acceptor forms.
heterochromatin. Regions of chromatin
that are highly condensed.
heterocyclic molecule. A molecule that contains a ring structure made up of more than
one type of atom.
heteroglycan (heteropolysaccharide). A carbohydrate polymer whose residues consist of
two or more different types of monosaccharide.
heterotroph. An organism that requires at
least one organic nutrient, such as glucose, as
a carbon source.
high density lipoprotein (HDL). A type of
plasma lipoprotein that is enriched in protein
and transports cholesterol and cholesteryl esters from tissues to the liver.
high-performance liquid chromatography
(HPLC). A chromatographic technique used
to separate components of a mixture by
dissolving the mixture in a liquid solvent and
forcing it to flow through a chromatographic
column under high pressure.
histones. A class of proteins that bind to
DNA to form chromatin. The nuclei of eukaryotic cells contain five histones, known as
H1, H2A, H2B, H3, and H4.
Holliday junction. The region of strand
crossover resulting from recombination between two molecules of homologous doublestranded DNA.
GLOSSARY OF BIOCHEMICAL TERMS
homoglycan (homopolysaccharide). A carbohydrate polymer whose residues consist of
a single type of monosaccharide.
homologous. Referring to genes or proteins
that descend from a common ancestor.
homologous recombination. Recombination
between molecules of DNA that have closely
related sequences (i.e., they are homologous).
This is the standard form of recombination
that occurs between chromosomes in eukaryotic cells.
homology. The similarity of genes or proteins as a result of evolution from a common
hormone response element. A DNA sequence that binds a transcriptional activator
consisting of a steroid hormone receptor
housekeeping genes. Genes that encode
proteins or RNA molecules that are essential
for the normal activities of all living cells.
HPLC. See high-performance liquid chromatography.
hydration. A state in which a molecule or
ion is surrounded by water.
hydrogen bond. A weak electrostatic interaction the formed when a hydrogen atom bonded
covalently to a strongly electronegative atom
is partially shared by interacting with electron
pair of another electronegative atom.
hydrolase. An enzyme that catalyzes the
hydrolytic cleavage of its substrate(s) (i.e.,
hydropathy. A measure of the hydrophobicity of amino acid side chains. The more positive the hydropathy value, the greater the
molecules that interact favorably with water.
hydrophilicity. The degree to which a compound or functional group interacts with
water or is preferentially soluble in water.
hydrophobic. “Water fearing”—describing
molecules that do not interact favorably with
water and are much less soluble than hydrophilic molecules.
hydrophobic effect. The exclusion of hydrophobic groups or molecules by water. The
hydrophobic effect appears to depend on the
increase in entropy of solvent water molecules that are released from an ordered
arrangement around the hydrophobic group.
hydrophobic interaction. A weak, noncovalent interaction between nonpolar molecules
or substituents that results from the strong
association of water molecules with one another. Such association leads to the shielding
or exclusion of nonpolar molecules from an
hydrophobicity. The degree to which a
compound or functional group that is soluble in nonpolar solvents is insoluble or only
sparingly soluble in water.
IDL. See intermediate density lipoprotein.
induced fit. Activation of an enzyme by a
substrate-initiated conformational change.
inducer. A ligand that binds to and inactivates
a repressor thereby increasing the transcription
of the gene controlled by the repressor.
inhibition constant (Ki). The equilibrium
constant for the dissociation of an inhibitor
from an enzyme-inhibitor complex.
inhibitor. A compound that binds to an enzyme and inhibits its activity.
initial velocity (v0). The rate of conversion
of substrate to product in the early stages of
an enzymatic reaction, before appreciable
product has been formed.
initiation codon. A codon that specifies the
initiation site for protein synthesis. The methionine codon (AUG) is the most common
initiation factor. See translation initiation
initiator tRNA. The tRNA molecule that is
used exclusively at initiation codons. The
initiator tRNA is usually a specific methionyl-tRNA.
integral membrane protein. A membrane
protein that penetrates the hydrophobic core
of the lipid bilayer and usually spans the bilayer completely. Also known as an intrinsic
intercalating agent. A compound containing a planar ring structure that can fit between the stacked base pairs of DNA.
Intercalating agents distort the DNA structure, partially unwinding the double helix.
intermediary metabolism. The metabolic
reactions by which the small molecules of
cells are interconverted.
intermediate density lipoprotein (IDL). A
type of plasma lipoprotein that is formed
during the breakdown of VLDLs.
intermediate filament. A structure composed of different protein subunits, found in
the cytoplasm of most eukaryotic cells. Intermediate filaments are components of the cytoskeletal network.
intron. An internal nucleotide sequence that
is removed from the primary RNA transcript
during processing. The term intron also
refers to the region of the gene that corresponds to the corresponding RNA intron
inverted repeat. A sequence of nucleotides
that is repeated in the opposite orientation
within the same polynucleotide strand. An
inverted repeat in double-stranded DNA can
give rise to a cruciform structure.
ion pair. An electrostatic interaction between
ionic groups of opposite charge within the interior of a macromolecule such as a globular
ion product for water (Kw). The product of
the concentrations of hydronium ions and
hydroxide ions in an aqueous solution, equal
to 1.0 * 10 - 14 M2.
ion-exchange chromatography. A chromatographic technique used to separate a mixture of
ionic species in solution, using a charged matrix. In anion-exchange chromatography, a
positively charged matrix binds negatively
charged solutes, and in cation-exchange chromatography, a negatively charged matrix binds
positively charged solutes. The bound species
can be serially eluted from the matrix by gradually changing the pH or increasing the salt
concentration in the solvent.
ionophore. A compound that facilitates the
diffusion of ions across bilayers and membranes by serving as a mobile ion carrier or
by forming a channel for ion passage.
irreversible enzyme inhibition. A form of
enzyme inhibition where the inhibitor binds
covalently to the enzyme.
isoacceptor tRNA molecules. Different tRNA
molecules that bind the same amino acid.
isoelectric focusing. A modified form of
electrophoresis that uses buffers to create a
pH gradient within a polyacrylamide gel.
Each protein migrates to its isoelectric point
(pI), that is, the pH in the gradient at which it
no longer carries a net positive or negative
isoelectric point (pI). The pH at which a
zwitterionic molecule does not migrate in an
electric field because its net charge is zero.
isoenzymes. See isozymes.
isomerase. An enzyme that catalyzes an isomerization reaction, a change in geometry or
structure within one molecule.
isoprene. A branched, unsaturated five-carbon molecule that forms the basic structural
unit of all isoprenoids, including the steroids
and lipid vitamins.
isoprenoid. A lipid that is structurally related
isozymes. Different proteins from a single
biological species that catalyze the same reaction. Also known as isoenzymes.
junk DNA. Regions of the genome with no
Ka. See acid dissociation constant.
kb. See kilobase pair.
kcat. See catalytic constant.
kcat>K m. The second-order rate constant
for conversion of enzyme and substrate to
enzyme and product at low substrate concentrations. The ratio of kcat to Km, when
used to compare several substrates, is called
the specificity constant.
Keq. See equilibrium constant.
ketogenesis. The pathway that synthesizes
ketone bodies from acetyl CoA in the mitochondrial matrix in mammals.
ketogenic compound. A compound, such as
an amino acid, that can be degraded to form
acetyl CoA and can thereby contribute to the
synthesis of fatty acids or ketone bodies.
ketone bodies. Small molecules that are
synthesized in the liver from acetyl CoA.
During starvation, the ketone bodies
b-hydroxybutyrate and acetoacetate become
major metabolic fuels.
GLOSSARY OF BIOCHEMICAL TERMS
ketoses. A class of monosaccharides in which
the most oxidized carbon atom, usually C-2,
Kj. See inhibition constant.
kilobase pair (kb). A unit of length of double-stranded DNA, equivalent to 1000 base
kinase. An enzyme that catalyzes transfer of
a phosphoryl group to an acceptor molecule.
A protein kinase catalyzes the phosphorylation of protein substrates. Kinases are also
known as phosphotransferases.
kinetic mechanism. A scheme used to describe the sequence of steps in a multisubstrate enzyme-catalyzed reaction.
kinetic order. The sum of the exponents in a
rate equation, which reflects how many molecules are reacting in the slowest step of the
reaction. Also known as reaction order.
Km. See Michaelis constant.
Krebs cycle. See citric acid cycle.
Kw. See ion product of water.
lagging strand. The newly synthesized DNA
strand formed by discontinuous 5¿ : 3¿
polymerization in the direction opposite
replication fork movement.
lateral diffusion. The rapid motion of lipid
or protein molecules within the plane of one
leaflet of a lipid bilayer.
LDL. See low density lipoprotein.
leader peptide. The peptide encoded by a portion of the leader region of certain regulated
operons. Synthesis of a leader peptide is the
basis for regulating transcription of the entire
operon by the mechanism of attenuation.
leader region. The sequence of nucleotides
that lie between the transcription start site
and the first coding region of an operon.
leading strand. The newly synthesized DNA
strand formed by continuous 5¿ : 3¿ polymerization in the same direction as replication fork movement.
leaflet. One layer of a lipid bilayer.
lectin. A plant protein that binds specific
saccharides in glycoproteins.
leucine zipper. A structural motif found in
DNA-binding proteins and other proteins.
The zipper is formed when the hydrophobic
faces (frequently containing leucine residues)
of two amphipathic a-helices from the same
or different polypeptide chains interact to
form a coiled-coil structure.
LHC. See light-harvesting complex.
ligand. A molecule, group, or ion that binds
noncovalently to another molecule or atom.
ligand-gated ion channel. A membrane ion
channel that opens or closes in response to
binding of a specific ligand.
ligase. An enzyme that catalyzes the joining,
or ligation, of two substrates. Ligation reactions require the input of the chemical potential energy of a nucleoside triphosphate such
as ATP. Ligases are commonly referred to as
light reactions. The photosynthetic reactions in which protons derived from water
are used in the chemiosmotic synthesis of
ATP from ADP + Pi and a hydride ion from
water reduces to NADPH. Also known as the
light-harvesting complex (LHC). A large
pigment complex in the thylakoid membrane
that aids a photosystem in gathering light.
limit dextrin. A branched oligosaccharide
derived from a glucose polysaccharide by the
hydrolytic action of amylase or the phosphorolytic action of glycogen phosphorylase or
starch phosphorylase. Limit dextrins are resistant to further degradation catalyzed by
amylase or phosphorylase. Limit dextrins can
be further degraded only after hydrolysis of
the a-(1 : 6) linkages.
Lineweaver-Burk plot. See double-reciprocal
linker DNA. The stretch of DNA (approximately 54 base pairs) between two adjacent
nucleosome core particles.
lipase. An enzyme that catalyzes the hydrolysis of triacylglycerols.
lipid. A water-insoluble (or sparingly soluble) organic compound found in biological
systems, which can be extracted by using relatively nonpolar organic solvents.
lipid bilayer. A double layer of lipids in
which the hydrophobic tails associate with
one another in the interior of the bilayer and
the polar head groups face outward into the
aqueous environment. Lipid bilayers are the
structural basis of biological membranes.
lipid raft. A patch of membrane rich in cholesterol and sphingolipid.
lipid vitamin. A polyprenyl compound composed primarily of a long hydrocarbon chain
or fused ring. Unlike water-soluble vitamins,
lipid vitamins can be stored by animals. Lipid
vitamins include vitamins A, D, E, and K.
lipid anchored membrane protein. A membrane protein that is tethered to a membrane through covalent linkage to a lipid
lipopolysaccharide. A macromolecule composed of lipid A (a disaccharide of phosphorylated glucosamine residues with attached fatty
acids) and a polysaccharide. Lipopolysaccharides are found in the outer membrane of
gram-negative bacteria. These compounds are
released from bacteria undergoing lysis and
are toxic to humans and other animals. Also
known as an endotoxin.
lipoprotein. A macromolecular assembly of
lipid and protein molecules with a hydrophobic core and a hydrophilic surface. Lipids are
transported via lipoproteins.
liposome. A synthetic vesicle composed of a
phospholipid bilayer that encloses an aqueous compartment.
loop. A nonrepetitive polypeptide region
that connects secondary structures within a
protein molecule and provides directional
changes necessary for a globular protein to
attain its compact shape. Loops contain from
2 to 16 residues. Short loops of up to 5
residues are often called turns.
low density lipoprotein (LDL). A type of
plasma lipoprotein that is formed during the
breakdown of IDLs and is enriched in cholesterol and cholesteryl esters.
lumen. The aqueous space enclosed by a biological membrane, such as the membrane of
the endoplasmic reticulum or the thylakoid
lyase. An enzyme that catalyzes a nonhydrolytic or nonoxidative elimination reaction,
or lysis, of a substrate, with the generation of a
double bond. In the reverse direction, a lyase
catalyzes addition of one substrate to a double
bond of a second substrate.
lipid that is produced when one of the two
fatty acyl moieties of a glycerophospholipid is
hydrolytically removed. Low concentrations
of lysophosphoglycerides are metabolic intermediates, whereas high concentrations
disrupt membranes, causing cells to lyse.
lysosome. A specialized digestive organelle
in eukaryotic cells. Lysosomes contain a variety of enzymes that catalyze the breakdown
of cellular biopolymers, such as proteins, nucleic acids, and polysaccharides, and the digestion of large particles, such as some
bacteria ingested by the cell.
major groove. The wide groove on the surface of a DNA double helix created by the
stacking of base pairs and the resulting twist
in the sugar-phosphate backbones.
MALDI. See matrix-assisted laser desorption ionization.
mass action ratio (Q). The ratio of the concentrations of products to the concentrations
of reactants of a reaction.
mass spectrometry. A technique that determines the mass of a molecule.
matrix. See mitochondrial matrix.
matrix-assisted laser desorption ionization
(MALDI). A technique in mass spectrometry where the target molecule is released from
a solid matrix by a laser beam.
maximum velocity (Vmax). The initial velocity of a reaction when the enzyme is saturated
with substrate, that is, when all the enzyme is
in the form of an enzyme-substrate complex.
melting curve. A plot of the change in absorbance versus temperature for a DNA molecule. The change in absorbance indicates
unfolding of the double helix.
melting point (Tm). The midpoint of the
temperature range in which double-stranded
DNA is converted to single-stranded DNA or
a protein is converted from its native form to
the denatured state.
membrane. A lipid bilayer containing associated proteins that serves to delineate and compartmentalize cells or organelles. Biological
membranes are also the site of many important
GLOSSARY OF BIOCHEMICAL TERMS
biochemical processes related to energy transduction and intracellular signaling.
membrane-associated electron transport.
See electron transport.
membrane potential (≤C). The charge separation across a membrane that results from
differences in ionic concentrations on the
two sides of the membrane.
messenger ribonucleic acid. See mRNA.
metabolic fuel. A small compound that can
be catabolized to release energy. In multicellular organisms, metabolic fuels may be transported between tissues.
metabolically irreversible reaction. A reaction in which the value of the mass action
ratio is two or more orders of magnitude
smaller than the value of the equilibrium
constant. The Gibbs free energy change for
such a reaction is a large negative number;
thus, the reaction is essentially irreversible.
metabolism. The sum total of biochemical
reactions carried out by an organism.
metabolite. An intermediate in the synthesis
or degradation of biopolymers and their
metabolite channeling. Transfer of the
product of one reaction of a multifunctional
enzyme or a multienzyme complex directly
to the next active site or enzyme without entering the bulk solvent. Channeling increases
the rate of a reaction pathway by decreasing
the transit time for an intermediate to reach
the next enzyme and by producing high local
concentrations of the intermediate.
metalloenzyme. An enzyme that contains
one or more firmly bound metal ions. In
some cases, such metal ions constitute part of
the active site of the enzyme and are active
participants in catalysis.
micelle. An aggregation of amphipathic
molecules in which the hydrophilic portions
of the molecules project into the aqueous
environment and the hydrophobic portions
associated with one another in the interior of
the structure to minimize contact with water
Michaelis constant (Km). The concentration of substrate that results in an initial
velocity (v0) equal to one-half the maximum
velocity (Vmax) for a given reaction.
Michaelis-Menten equation. A rate equation
relating the initial velocity (v0) of an enzymatic reaction to the substrate concentration
([S]), the maximum velocity (Vmax), and the
Michaelis constant (Km).
microfilament. See actin filament.
microtubule. A protein filament composed
of a and b tubulin heterodimers. Microtubules are components of the cytoskeletal
network and can form structures capable of
minor groove. The narrow groove on the
surface of a DNA double helix created by the
stacking of base pairs and the resulting twist
in the sugar-phosphate backbones.
mismatch repair. Restoration of the normal
nucleotide sequence in a DNA molecule containing mismatched bases. In mismatch repair, the correct strand is recognized, a
portion of the incorrect strand is excised, and
correctly base-paired, double-stranded DNA
is synthesized by the actions of DNA polymerase and DNA ligase.
missense mutation. An alteration in DNA
that involves the substitution of one nucleotide for another, resulting in a change in
the amino acid specified by that codon.
mitochondrial matrix. The gel-like phase
enclosed by the inner membrane of the mitochondrion. The mitochondrial matrix contains many enzymes involved in aerobic
mitochondrion. An organelle that is the
main site of oxidative energy metabolism in
most eukaryotic cells. Mitochondria contain
an outer and an inner membrane, the latter
characteristically folded into cristae.
mixed inhibition. A form of enzyme inhibition where both Km and Vmax are affected.
molar mass. The weight in grams of one
mole of a compound.
molecular chaperone. See chaperone.
molecular crowding. The decrease in diffusion rate that occurs when molecules collide
with each other.
molecular weight. See relative molecular
monocistronic mRNA. An mRNA molecule
that encodes only a single polypeptide. Most
eukaryotic mRNA molecules are monocistronic.
monomer. 1. A small compound that becomes a residue when polymerized with
other monomers. 2. A single subunit of a
monosaccharide. A simple sugar of three or
more carbon atoms with the empirical formula (CH2O)n.
monounsaturated fatty acid. An unsaturated
fatty acid with a single carbon-carbon double
motif. A combination of secondary structure
that appears in a number of different proteins.
Also known as supersecondary structure.
Mr. See relative molecular mass.
mRNA. A class of RNA molecules that serve
as templates for protein synthesis.
mRNA precursor. A class of RNA molecules
synthesized by eukaryotic RNA polymerase
II. mRNA precursors are processed posttranscriptionally to produce mature messenger
mucin. A high-molecular-weight O-linked
glycoprotein containing as much as 80% carbohydrate by mass. Mucins are extended,
negatively charged molecules that contribute
to the viscosity of mucus, the fluid found on
the surfaces of the gastrointestinal, genitourinary, and respiratory tracts.
multienzyme complex. An oligomeric protein that catalyzes several metabolic reactions.
mutagen. An agent that can cause DNA
mutation. A heritable change in the sequence of nucleotides in DNA that causes a
permanent alteration of genetic information.
near-equilibrium reaction. A reaction in
which the value of the mass action ratio is
close to the value of the equilibrium constant.
The Gibbs free energy change for such a reaction is small; thus, the reaction is reversible.
Nernst equation. An equation that relates
the observed change in reduction potential
(¢E) to the change in standard reduction potential (¢E°¿) of a reaction.
neutral phospholipids. Glycerophospholipids,
such as phosphatidyl choline, having no net
neutral solution. An aqueous solution that
has a pH value of 7.0.
nick translation. The process in which DNA
polymerase binds to a gap between the 3¿ end
of a nascent DNA chain and the 5¿ end of the
next RNA primer, catalyzes hydrolytic removal of ribonucleotides using 5¿ : 3¿ exonuclease activity, and replaces them with
deoxyribonucleotides using 5¿ : 3¿ polymerase activity.
nitrogen cycle. The flow of nitrogen from
N2 to nitrogen oxides (NO2ᮎ and NO3ᮎ ) ammonia, nitrogenous biomolecules, and back
nitrogen fixation. The reduction of atmospheric nitrogen to ammonia. Biological nitrogen fixation occurs in only a few species of
bacteria and algae.
N-linked oligosaccharide. An oligosaccharide chain attached to a protein through covalent bonds to the amide nitrogen atom of
side chain of asparagine residues. The
oligosaccharide chains of N-linked glycoproteins contain a core pentasaccharide of two
N-acetylglucosamine residues and three
NMR spectroscopy. See nuclear magnetic
noncompetitive inhibition. Inhibition of an
enzyme-catalyzed reaction by a reversible inhibitor that binds to either the enzyme or the
enzyme- substrate complex.
nonessential amino acid. An amino acid
that an animal can produce in sufficient
quantity to meet metabolic needs.
nonhomologous recombination. Recombination between unrelated sequences that do not
share significant sequence similarity.
nonrepetitive structure. An element of protein structure in which consecutive residues
do not have a single repeating conformation.
nonsense mutation. An alteration in DNA
that involves the substitution of one nucleotide for another, changing a codon that
specifies an amino acid to a termination
GLOSSARY OF BIOCHEMICAL TERMS
codon. A nonsense mutation results in premature termination of a protein’s synthesis.
N-terminus. The amino acid residue bearing a free a-amino group at one end of a peptide chain. In some proteins, the N-terminus
is blocked by acylation. The N-terminal
residue is usually assigned the residue number 1. Also known as the amino terminus.
nuclear envelope. The double membrane
that surrounds the nucleus and contains protein-lined nuclear pore complexes that regulate the import and export of material to and
from the nucleus. The outer membrane of
the nuclear envelope is continuous with the
endoplasmic reticulum; the inner membrane
is lined with filamentous proteins, constituting the nuclear lamina.
nuclear magnetic resonance spectroscopy
(NMR spectroscopy). A technique used to
study the structures of molecules in solution.
In nuclear magnetic resonance spectroscopy,
the absorption of electromagnetic radiation
by molecules in magnetic fields of varying
frequencies is used to determine the spin
states of certain atomic nuclei.
nuclease. An enzyme that catalyzes hydrolysis of the phosphodiester linkages of a
polynucleotide chain. Nucleases can be classified as endonucleases and exonucleases.
nucleic acid. A polymer composed of nucleotide residues linked in a linear sequence
by 3¿ –5¿ phosphodiester linkages. DNA and
RNA are nucleic acids composed of deoxyribonucleotide residues and ribonucleotide
nucleoid region. The region within a prokaryotic cell that contains the chromosome.
nucleolus. The region of the eukaryotic nucleus where rRNA transcripts are processed
and ribosomes are assembled.
nucleophile. An electron-rich species that is
negatively charged or contains unshared electron pairs and is attracted to chemical species
that are positively charged or electron-deficient (electrophiles).
nucleophilic substitution. A reaction in
which one nucleophile (e.g., Y ᮎ ) displaces
another (e.g., X ᮎ ).
nucleoside. A purine or pyrimidine N-glycoside of ribose or deoxyribose.
nucleosome. A DNA-protein complex that
forms the fundamental unit of chromatin. A
nucleosome consists of a nucleosome core
particle (approximately 146 base pairs of
DNA plus a histone octamer), linker DNA
(approximately 54 base pairs), and histone
H1 (which binds the core particle and linker
nucleosome core particle. A DNA-protein
complex composed of approximately 146
base pairs of DNA wrapped around an octamer of histones (two each of H2A, H2B,
H3, and H4).
nucleotide. The phosphate ester of a nucleoside, consisting of a nitrogenous base linked
to a pentose phosphate. Nucleotides are the
monomeric units of nucleic acids.
nucleus. An organelle that contains the
principal genetic material of eukaryotic cells
and functions as the major site of RNA synthesis and processing.
obligate aerobe. An organism that requires
the presence of oxygen for survival.
obligate anaerobe. An organism that requires
an oxygen-free environment for survival.
Okazaki fragments. Relatively short strands
of DNA that are produced during discontinuous synthesis of the lagging strand of DNA.
oligomer. A multisubunit molecule whose
arrangement of subunits always has a defined
stoichiometry and almost always displays
oligonucleotide. A polymer of several (up to
about 20) nucleotide residues linked by phosphodiester bonds.
oligopeptide. A polymer of several (up to
about 20) amino acid residues linked by
oligosaccharide. A polymer of 2 to about 20
monosaccharide residues linked by glycosidic
oligosaccharide processing. The enzymecatalyzed addition and removal of saccharide
residues during the maturation of a glycoprotein.
O-linked oligosaccharide. An oligosaccharide attached to a protein through a covalent
bond to the hydroxyl oxygen atom of a serine
or threonine residue.
open reading frame. A stretch of nucleotide
triplets that contains no termination codons.
Protein-encoding regions are examples of
open reading frames.
operator. A DNA sequence to which a specific repressor protein binds, thereby blocking transcription of a gene or operon.
operon. A bacterial transcriptional unit
consisting of several different coding regions
cotranscribed from one promoter.
ordered sequential reaction. A reaction in
which both the binding of substrates to an
enzyme and the release of products from the
enzyme follow an obligatory order.
organelle. Any specialized membranebounded structure within a eukaryotic cell.
Organelles are uniquely organized to perform specific functions.
origin of replication. A DNA sequence at
which replication is initiated.
osmosis. The movement of solvent molecules from a less concentrated solution to an
adjacent, more concentrated solution.
osmotic pressure. The pressure required to
prevent the flow of solvent from a less concentrated solution to a more concentrated
oxidase. An enzyme that catalyzes an oxidation-reduction reaction in which O2 is the
electron acceptor. Oxidases are members of
the IUBMB class of enzymes known as oxidoreductases.
oxidation. The loss of electrons from a substance through transfer to another substance
(the oxidizing agent). Oxidations can take
several forms, including the addition of oxygen to a compound, the removal of hydrogen
from a compound to create a double bond, or
an increase in the valence of a metal ion.
oxidative phosphorylation. See electron
oxidizing agent. A substance that accepts
electrons in an oxidation-reduction reaction
and thereby becomes reduced.
oxidoreductase. An enzyme that catalyzes an
oxidation-reduction reaction. Some oxidoreductases are known as dehydrogenases, oxidases, peroxidases, oxygenases, or reductases.
oxygenation. The reversible binding of oxygen to a macromolecule.
≤p. See protonmotive force.
PAGE. See polyacrylamide gel electrophoresis.
passive transport. The process by which a
solute specifically binds to a transport protein and is transported across a membrane,
moving with the solute concentration gradient. Passive transport occurs without the expenditure of energy. Also known as facilitated
Pasteur effect. The slowing of glycolysis in
the presence of oxygen.
pathway. A sequence of metabolic reactions.
pause site. A region of a gene where transcription slows. Pausing is exaggerated at
palindromic sequences, where newly synthesized RNA can form a hairpin structure.
PCR. See polymerase chain reaction.
pentose phosphate pathway. A pathway by
which glucose 6-phosphate is metabolized to
generate NADPH and ribose 5-phosphate. In
the oxidative stage of the pathway, glucose 6phosphate is converted to ribulose 5-phosphate
and CO2 rating two molecules of NADPH. In
the nonoxidative stage, ribulose 5-phosphate
can be isomerized to ribose 5-phosphate or
converted to intermediates of glycolysis. Also
known as the hexose monophosphate shunt.
peptide. Two or more amino acids covalently
joined in a linear sequence by peptide bonds.
peptide bond. The covalent secondary
amide linkage that joins the carbonyl group
of one amino acid residue to the amino nitrogen of another in peptides and proteins.
peptide group. The nitrogen and carbon
atoms involved in a peptide bond and their
four substituents: the carbonyl oxygen atom,
the amide hydrogen atom, and the two adjacent a-carbon atoms.
peptidoglycan. A macromolecule containing a heteroglycan chain of alternating Nacetylglucosamine and N-acetylmuramic
acid cross-linked to peptides of varied composition. Peptidoglycans are the major components of the cell walls of many bacteria.
peptidyl site. See P site.
GLOSSARY OF BIOCHEMICAL TERMS
peptidyl transferase. The enzymatic activity
responsible for the formation of a peptide
bond during protein synthesis.
peptidyl-tRNA. The tRNA molecule to
which the growing peptide chain is attached
during protein synthesis.
peripheral membrane protein. A membrane
protein that is weakly bound to the interior or
exterior surface of a membrane through ionic
interactions and hydrogen bonding with the
polar heads of the membrane lipids or with an
integral membrane protein. Also known as an
extrinsic membrane protein.
periplasmic space. The region between the
plasma membrane and the cell wall in bacteria.
permeability coefficient. A measure of the
ability of an ion or small molecule to diffuse
across a lipid bilayer.
peroxisome. An organelle in all animal and
many plant cells that carries out oxidation reactions, some of which produce the toxic
compound hydrogen peroxide (H2O2). Peroxisomes contain the enzyme catalase, which
catalyzes the breakdown of toxic H2O2 to
water and O2.
pH. A logarithmic quantity that indicates
the acidity of a solution, that is, the concentration of hydronium ions in solution. pH is
defined as the negative logarithm of the hydronium ion concentration.
pH optimum. In an enzyme-catalyzed reaction, the pH at the point of maximum
phage. See bacteriophage.
phase-transition temperature (Tm). The
midpoint of the temperature range in which
lipids or other macromolecular aggregates
are converted from a highly ordered phase or
state (such as a gel) to a less-ordered state
(such as a liquid crystal).
F (phi). The angle of rotation around the
bond between the a-carbon and the nitrogen
of a peptide group.
phosphagen. A “high energy” phosphate
storage molecule found in animal muscle
cells. Phosphagens are phosphoamides and
have a higher phosphoryl-group-transfer
potential than ATP.
phosphatase. An enzyme that catalyzes
the hydrolytic removal of a phosphoryl
phosphatidate. A glycerophospholipid that
consists of two fatty acyl groups esterified to
C-1 and C-2 of glycerol 3-phosphate. Phosphatidates are metabolic intermediates in the
biosynthesis or breakdown of more complex
phosphoanhydride. A compound formed
by condensation of two phosphate groups.
phosphodiester linkage. A linkage in nucleic
acids and other molecules in which two alcoholic hydroxyl groups are joined through a
phosphoester linkage. The bond by which a
phosphoryl group is attached to an alcoholic
or phenolic oxygen.
phospholipid. A lipid containing a phosphate moiety.
phosphorolysis. Cleavage of a bond within
a molecule by group transfer to an oxygen
atom of phosphate.
phosphorylase. An enzyme that catalyzes
the cleavage of its substrate(s) via nucleophilic attack by inorganic phosphate (Pi)
(i.e., via phosphorolysis).
phosphorylation. A reaction involving the
addition of a phosphoryl group to a molecule.
phosphoryl group transfer potential. A
measure of the ability of a compound to
transfer a phosphoryl group to another compound. Under standard conditions, group
transfer potentials have the same values as
the standard free energies of hydrolysis but
are opposite in sign.
photoautotroph. A photosynthetic organism that can utilize CO2 as its main carbon
photon. A quantum of light energy.
photophosphorylation. The light-dependent
formation of ATP from ADP and Pi catalyzed
by chloroplast ATP synthase.
photoheterotroph. Photosynthetic organism that requires organic molecules as a carbon source.
photoreactivation. The direct repair of
damaged DNA by an enzyme that is activated
by visible light.
photorespiration. The light-dependent uptake of O2 and the subsequent metabolism of
phosphoglycolate that occurs primarily in C3
photosynthetic plants. Photorespiration can
occur because O2 competes with CO2 for
the active site of ribulose 1,5-bisphosphate
carboxylase-oxygenase, the enzyme that catalyzes the first step of the reductive pentose
photosynthesis. The conversion of light energy (photons) to chemical energy in the
form of ATP and/or NADPH.
photosystem. A functional unit of the lightdependent electron-transfer reactions of
photosynthesis. Each membrane-embedded
photosystem contains a reaction center, which
forms the core of the photosystem, and a pool
of light-absorbing antenna pigments.
phototroph. An organism that can convert
light energy into chemical potential energy
(i.e., an organism capable of photosynthesis).
physiological pH. The normal pH of human
blood, which is 7.4.
pI. See isoelectric point.
ping-pong reaction. A reaction in which an
enzyme binds one substrate and releases a
product, leaving a substituted enzyme that
then binds a second substrate and releases a
second product, thereby restoring the enzyme to its original form.
pitch. The axial distance for one complete
turn of a helical structure.
pKa. A logarithmic value that indicates the
strength of an acid. pKa is defined as the
negative logarithm of the acid dissociation
plasma membrane. The membrane that
surrounds the cytoplasm of a cell and thus
defines the perimeter of the cell.
plasmalogen. A glycerophospholipid that
has a hydrocarbon chain linked to C-1 of
glycerol 3-phosphate through a vinyl ether
linkage. Plasmalogens are found in the central nervous system and in peripheral nerve
and muscle tissue.
plasmid. A relatively small, extrachromosomal DNA molecule that is capable of autonomous replication. Plasmids are usually
closed, circular, double-stranded DNA
P:O ratio. The ratio of molecules of ADP
phosphorylated to atoms of oxygen reduced
during oxidative phosphorylation.
polar. Having uneven distribution of charge.
A molecule or functional group is polar if its
center of negative charge does not coincide
with its center of positive charge.
poly A tail. A stretch of polyadenylate, up to
250 nucleotide residues long, that is added to
the 3¿ end of a eukaryotic mRNA molecule
polyacrylamide gel electrophoresis (PAGE).
A technique used to separate molecules of
different net charge and/or size based on
their migration through a highly cross-linked
gel matrix in an electric field.
polycistronic mRNA. An mRNA molecule
that contains multiple coding regions. Many
prokaryotic mRNA molecules are polycistronic.
polymerase chain reaction (PCR). A
method for amplifying the amount of DNA in
a sample and for enriching a particular DNA
sequence in a population of DNA molecules.
In the polymerase chain reaction, oligonucleotides complementary to the ends of the
desired DNA sequence are used as primers for
multiple rounds of DNA synthesis.
polynucleotide. A polymer of many (usually
more than 20) nucleotide residues linked by
polypeptide. A polymer of many (usually
more than 20) amino acid residues linked by
polyribosome. See polysome.
polysaccharide. A polymer of many (usually
more than 20) monosaccharide residues
linked by glycosidic bonds. Polysaccharide
chains can be linear or branched.
polysome. The structure formed by the
binding of many translation complexes to a
large mRNA molecule. Also known as a
polyunsaturated fatty acid. An unsaturated
fatty acid with two or more carbon-carbon
pore. See channel.
posttranscriptional processing. RNA processing that occurs after transcription is
GLOSSARY OF BIOCHEMICAL TERMS
posttranslational modification. Covalent
modification of a protein that occurs after
synthesis of the polypeptide is complete.
prenylated protein. A lipid-anchored protein that is covalently linked to an isoprenoid
moiety via the sulfur atom of a cysteine
residue at the C-terminus of the protein.
primary structure. The sequence in which
residues are covalently linked to form a polymeric chain.
primary transcript. A newly synthesized
RNA molecule before processing.
primase. An enzyme in the primosome that
catalyzes the synthesis of short pieces of RNA
about 10 residues long. These oligonucleotides are the primers for synthesis of
primosome. A multiprotein complex, including primase and helicase in E. coli, that
catalyzes the synthesis of the short RNA
primers needed for discontinuous DNA synthesis of the lagging strand.
processive enzyme. An enzyme that remains bound to its growing polymeric
product through many polymerization steps
(cf., distributive enzyme).
prochiral atom. An atom with multiple substituents, two of which are identical. A
prochiral atom can become chiral when one
of the identical substituents is replaced.
prokaryote. An organism, usually a single
cell, which contains no nucleus or internal
membranes (cf., eukaryote).
promoter. The region of DNA where RNA
polymerase binds during transcription
prostaglandin. An eicosanoid that has a cyclopentane ring. Prostaglandins are metabolic regulators that act in the immediate
neighborhood of the cells in which they are
prosthetic group. A coenzyme that is tightly
bound to an enzyme. A prosthetic group, unlike a cosubstrate, remains bound to a specific site of the enzyme throughout the
catalytic cycle of the enzyme.
protease. An enzyme that catalyzes hydrolysis of peptide bonds. The physiological substrates of proteases are proteins.
protein. A biopolymer consisting of one or
more polypeptide chains. The biological
function of each protein molecule depends
not only on the sequence of covalently linked
amino acid residues, but also on its threedimensional structure (conformation).
protein coenzyme. A protein that does not
itself catalyze reactions but is required for the
action of certain enzymes.
protein glycosylation. The covalent addition
of carbohydrate to proteins. In N-glycosylation, the carbohydrate is attached to the
amide group of the side chain of an asparagine residue. In O-glycosylation, the carbohydrate is attached to the hydroxyl group of
the side chain of a serine or threonine residue.
protein kinase. See kinase.
protein phosphatase. See phosphatase.
proteoglycan. A complex of protein with
glycosaminoglycan chains covalently bound
through their anomeric carbon atoms. Up to
95% of the mass of a proteoglycan may be
proteomics. The study of all proteins produced in a certain cell type, tissue, organ, or
protonmotive force (≤p). The energy
stored in a proton concentration gradient
across a membrane.
proximity effect. The increase in the rate of
a nonenzymatic or enzymatic reaction attributable to high effective concentrations of reactants, which result in more frequent
formation of transition states.
pseudo first-order reaction. A multi-reactant
reaction carried out under conditions where
the rate depends on the concentration of only
pseudogene. A nonexpressed sequence of
DNA that evolved from a protein-encoding
gene. Pseudogenes often contain mutations
in their coding regions and cannot produce
C (psi). The angle of rotation around the
bond between the a-carbon and the carbonyl
carbon of a peptide group.
≤C . See membrane potential.
P site. Peptidyl site. The site on a ribosome
that is occupied during protein synthesis by a
tRNA molecule attached to the growing
polypeptide chain (peptidyl tRNA).
purine. A nitrogenous base having a tworing structure in which a pyrimidine is fused
to imidazole. Adenine and guanine are substituted purines found in both DNA and RNA.
pyranose. A monosaccharide structure that
forms a six-membered ring as a result of intramolecular hemiacetal formation.
pyrimidine. A nitrogenous base having a
heterocyclic ring that consists of four carbon
atoms and two nitrogen atoms. Cytosine,
thymine, and uracil are substituted pyrimidines found in nucleic acids (cytosine in
DNA and RNA, uracil in RNA, and thymine
principally in DNA).
Q. See mass action ratio.
Q cycle. A cyclic pathway proposed to explain
the sequence of electron transfers and proton
movements within Complex III of mitochondria or the cytochrome bf complex in chloroplasts. The net result of the two steps of the
Q cycle is oxidation of two molecules of QH2
or plastoquinol (PQH2); formation of one
molecule of QH2 or PQH2; transfer of two
electrons; and net translocation of four protons across the inner mitochondrial membrane to the intermembrane space or across
the thylakoid membrane to the lumen.
quaternary structure. The organization of
two or more polypeptide chains within a
R state. The more active conformation of an
allosteric protein; opposite of T state.
Ramachandran plot. A plot of c versus f values for amino acid residues in a polypeptide
chain. Certain f and c values are characteristic of different conformations.
random sequential reaction. A reaction in
which neither the binding of substrates to an
enzyme nor the release of products from the
enzyme follows an obligatory order.
rate acceleration. The ratio of the rate constant for a reaction in the presence of enzyme
(kcat) divided by the rate constant for that reaction in the absence of enzyme (kn). The
rate acceleration value is a measure of the efficiency of an enzyme.
rate equation. An expression of the observed
relationship between the velocity of a reaction
and the concentration of each reactant.
rate determining step. The slowest step in a
chemical reaction. The rate determining step
has the highest activation energy among the
steps leading to formation of a product from
reaction center. A complex of proteins, electron transport cofactors, and a special pair
of chlorophyll molecules that forms the
core of a photosystem. The reaction center
is the site of conversion of photochemical
energy to electrochemical energy during
reaction mechanism. The step-by-step
atomic or molecular events that occur during
reaction order. See kinetic order.
reaction specificity. The lack of formation
of wasteful by-products by an enzyme. Reaction specificity results in essentially 100%
reactive center. The part of a coenzyme to
which mobile metabolic groups are attached.
reading frame. The sequence of nonoverlapping codons of an mRNA molecule that specifies the amino acid sequence. The reading
frame of an mRNA molecule is determined by
the position where translation begins; usually
an AUG codon.
receptor. A protein that binds a specific
ligand, such as a hormone, leading to some
recombinant DNA. A DNA molecule that
includes DNA from different sources.
recombination. See genetic recombination.
reducing agent. A substance that loses electrons in an oxidation-reduction reaction and
thereby becomes oxidized.
reducing end. The residue containing a free
anomeric carbon in a polysaccharide. A polysaccharide usually contains no more than
one reducing end.
reduction. The gain of electrons by a substance through transfer from another substance (the reducing agent). Reductions can
take several forms, including the loss of oxygen from a compound, the addition of
GLOSSARY OF BIOCHEMICAL TERMS
hydrogen to a double bond of a compound,
or a decrease in the valence of a metal ion.
reduction potential (E). A measure of the
tendency of a substance to reduce other substances. The more negative the reduction potential, the greater the tendency to donate
regulated enzyme. An enzyme located at a
critical point within one or more metabolic
pathways, whose activity may be increased or
decreased based on metabolic demand. Most
regulated enzymes are oligomeric.
regulatory protein. A protein that is involved in the regulation of gene expression,
usually at the point of transcription initiation. Repressors and activators are examples
of regulatory proteins.
regulatory site. A ligand-binding site in a
regulatory enzyme distinct from the active
site. Allosteric modulators alter enzyme activity by binding to the regulatory site. Also
known as an allosteric site.
relative molecular mass (Mr). The mass of a
molecule relative to 1/12th the mass of 12C.
There are no units associated with the values
for relative molecular mass.
release factor. A protein involved in terminating protein synthesis.
renaturation. The restoration of the native
conformation of a biological macromolecule,
usually resulting in restoration of biological
replication. The duplication of doublestranded DNA, during which parental strands
separate and serve as templates for synthesis
of new strands. Replication is carried out by
DNA polymerase and associated factors.
replication fork. The Y-shaped junction
where double-stranded, template DNA is
unwound and new DNA strands are synthesized during replication.
replisome. A multiprotein complex that includes DNA polymerase, primase, helicase,
single-strand binding protein, and additional
components. The replisomes, located at each
of the replication forks, carry out the polymerization reactions of bacterial chromosomal DNA replication.
repressor. A regulatory DNA-binding protein that prevents transcription by RNA
residue. A single component within a polymer. The chemical formula of a residue is
that of the corresponding monomer minus
the elements of water.
resonance energy transfer. A form of excitation energy transfer between molecules
that does not involve transfer of an electron.
respiratory electron transport chain. A
series of enzyme complexes and associated
cofactors that are electron carriers, passing
electrons from reduced coenzymes or
substrates to molecular oxygen (O2), the
terminal electron acceptor of aerobic
restriction endonuclease. An endonuclease
that catalyzes the hydrolysis of double-stranded DNA at a specific nucleotide sequence.
Type I restriction endonucleases catalyze both
the methylation of host DNA and the cleavage
of nonmethylated DNA, whereas type II restriction endonucleases catalyze only the
cleavage of nonmethylated DNA.
restriction map. A diagram showing the size
and arrangement of fragments produced
from a DNA molecule by the action of various restriction endonucleases.
reverse transcriptase. A type of DNA polymerase that catalyzes the synthesis of a strand
of DNA from an RNA template.
reverse turn. See turn.
ribonucleic acid (RNA). A polymer consisting of ribonucleotide residues joined by
3¿ – 5¿ phosphodiester bonds. The sugar moiety in RNA is ribose. Genetic information
contained in DNA is transcribed in the synthesis of RNA, some of which (mRNA) is
translated in the synthesis of protein.
ribonucleoprotein. A complex containing
both ribonucleic acid and protein.
ribosome. A large ribonucleoprotein complex composed of multiple ribosomal RNA
molecules and proteins. Ribosomes are the
site of protein synthesis.
ribozyme. An RNA molecule with enzymatic
rise. The distance between one residue and
the next along the axis of a helical macromolecule.
RNA processing. The reactions that transform a primary RNA transcript into a mature RNA molecule. The three general types
of RNA processing include the removal of
RNA nucleotides from primary transcripts,
the addition of RNA nucleotides not encoded by the gene, and the covalent modification of bases.
rRNA. See ribosomal ribonucleic acid.
S. See Svedberg unit.
S. See entropy.
salt bridge. See charge-charge interactions.
salvage pathway. A pathway in which a
major metabolite, such as a purine or pyrimidine nucleotide, can be synthesized from a
preformed molecular entity, such as a purine
saturated fatty acid. A fatty acid that does
not contain a carbon-carbon double bond.
Schiff base. A complex formed by the reversible condensation of a primary amine
with an aldehyde (to form an aldimine) or a
ketone (to form a ketimine).
SDS-PAGE. See sodium dodecyl sulfate–polyacrylamide gel electrophoresis.
second messenger. A compound that acts
intracellularly in response to an extracellular
secondary structure. The regularities in
local conformations within macromolecules.
In proteins, secondary structure is maintained by hydrogen bonds between carbonyl
and amide groups of the backbone. In nucleic acids, secondary structure is maintained by
hydrogen bonds and stacking interactions
between the bases.
second-order reaction. A reaction whose
rate depends on the concentrations of two reactants.
self-splicing intron. An intron that is excised in a reaction mediated by the RNA precursor itself.
sense strand. In double-stranded DNA the
sense strand is the strand that contains
codons. Also called the coding strand. The
opposite strand is called the antisense strand
or the template strand.
sequential reaction. An enzymatic reaction in which all the substrates must be
bound to the enzyme before any product is
sequential theory of cooperativity and allosteric regulation. A model of the cooperative binding of identical ligands to oligomeric
proteins. According to the simplest form of
the sequential theory, the binding of a ligand
may induce a change in the tertiary structure
of the subunit to which it binds and may
alter the conformations of neighboring subunits to varying extents. Only one subunit
conformation has a high affinity for the
ligand. Also known as the ligand-induced
Shine-Dalgarno sequence. A purine-rich
region just upstream of the initiation codon
in prokaryotic mRNA molecules. The ShineDalgarno sequence binds to a pyrimidinerich sequence in the ribosomal RNA, thereby
positioning the ribosome at the initiation
S factor. See s subunit.
S subunit (sigma subunit). A subunit of
prokaryotic RNA polymerase, which acts as a
transcription initiation factor by binding to
the promoter. Different s subunits are specific for different promoters. Also known as a
signal peptidase. An integral membrane
protein of the endoplasmic reticulum that
catalyzes cleavage of the signal peptide of
proteins translocated to the lumen.
signal peptide. The N-terminal sequence of
residues in a newly synthesized polypeptide
that targets the protein for translocation
across a membrane.
signal transduction. The process whereby
an extracellular signal is converted to an intracellular signal by the action of a membrane-associated receptor, a transducer, and
an effector enzyme.
signal recognition particle (SRP). A eukaryotic protein-RNA complex that binds a
newly synthesized peptide as it is extruded
from the ribosome. The signal-recognition
particle is involved in anchoring the ribosome to the cytosolic face of the endoplasmic
GLOSSARY OF BIOCHEMICAL TERMS
reticulum so that protein translocation to the
lumen can occur.
single-strand binding protein (SSB). A protein that binds tightly to single-stranded
DNA, preventing the DNA from folding back
on itself to form double-stranded regions.
site-directed mutagenesis. An in vitro procedure by which one particular nucleotide
residue in a gene is replaced by another, resulting in production of an altered protein
site-specific recombination. An example of
recombination that occurs at specific sites in
small nuclear ribonucleoprotein (snRNP).
An RNA-protein complex composed of one
or two specific snRNA molecules plus a number of proteins. snRNPs are involved in splicing mRNA precursors and in other cellular
small RNA. A class of RNA molecules. Some
small RNA molecules have catalytic activity.
Some small nuclear RNA molecules (snRNA)
are components of small nuclear ribonucleoproteins (snRNPs).
snRNA. See small nuclear RNA.
snRNP. See small nuclear ribonucleoprotein.
sodium dodecyl sulfate–polyacrylamide gel
electrophoresis (SDS-PAGE). Polyacrylamide
gel electrophoresis performed in the presence
of the detergent sodium dodecyl sulfate. SDSPAGE allows separation of proteins on the
basis of size only rather than charge and size.
solvation. A state in which a molecule or ion
is surrounded by solvent molecules.
solvation sphere. The shell of solvent molecules that surrounds an ion or solute.
special pair. A specialized pair of chlorophyll molecules in reaction centers that is the
primary electron donor during the light-dependent reactions of photosynthesis.
specific heat. The amount of heat required
to raise the temperature of 1 gram of a substance by 1°C.
specificity constant. See kcat>Km.
sphingolipid. An amphipathic lipid with a
sphingosine (trans-4-sphingenine) backbone. Sphingolipids, which include sphingomyelins, cerebrosides, and gangliosides, are
present in plant and animal membranes and
are particularly abundant in the tissues of the
central nervous system.
sphingomyelin. A sphingolipid that consists
of phosphocholine attached to the C-1 hydroxyl group of a ceramide. Sphingomyelins
are present in the plasma membranes of most
mammalian cells and are a major component
of myelin sheaths.
splice site. The conserved nucleotide sequence surrounding an exon-intron junction.
It includes the site where the RNA molecule is
cleaved during intron excision.
spliceosome. The large protein-RNA complex that catalyzes the removal of introns from
mRNA precursors. The spliceosome is composed of small nuclear ribonucleoproteins.
splicing. The process of removing introns
and joining exons to form a continuous RNA
SRP. See signal recognition particle.
SSB. See single-strand binding protein.
stacking interactions. The weak noncovalent
forces between adjacent bases or base pairs in
single-stranded or double-stranded nucleic
acids, respectively. Stacking interactions contribute to the helical shape of nucleic acids.
standard Gibbs free energy change (≤G° œ ).
The free energy change for a reaction under
biochemical standard state conditions.
standard reduction potential (E° œ ). A
measure of the tendency of a substance to reduce other substances under biochemical
standard state conditions.
standard state. A set of reference conditions
for a chemical reaction. In biochemistry, the
standard state is defined as a temperature of
298 K (25°C), a pressure of 1 atmosphere, a
solute concentration of 1.0 M, and a pH of 7.0.
starch. A homopolymer of glucose residues
that is a storage polysaccharide in plants.
There are two forms of starch: amylose, an
unbranched polymer of glucose residues
joined by a-(1 : 4) linkages; and amylopectin, a branched polymer of glucose
residues joined by a-(1 : 4) linkages with
a-(1 : 6) linkages at branch points.
steady state. A state in which the rate of synthesis of a compound is equal to its rate of
utilization or degradation.
stem-loop. See hairpin.
stereoisomers. Compounds with the same
molecular formula but different spatial
arrangements of their atoms.
stereospecificity. The ability of an enzyme
to recognize and act upon only a single
stereoisomer of a substrate.
steroid. A lipid containing a fused, four-ring
sterol. A steroid containing a hydroxyl group.
stomata. Structures on the surface of a leaf
through which carbon dioxide diffuses directly into photosynthetic cells.
stop codon. See termination codon.
strand invasion. The exchange of single
strands of DNA from two nicked molecules
having homologous nucleotide sequences.
stroma. The interior of a chloroplast corresponding to the cytoplasm of the ancestral
stromal lamellae. Regions of the thylakoid
membrane that are in contact with the stroma.
substrate. A reactant in a chemical reaction.
In enzymatic reactions, substrates are specifically acted upon by enzymes, which catalyze
the conversion of substrates to products.
substrate cycle. A pair of opposing reactions
that catalyzes a cycle between two pathway
substrate level phosphorylation. Phosphorylation of a nucleoside diphosphate by
transfer of a phosphoryl group from a nonnucleotide substrate.
supercoil. A topological arrangement assumed
by over- or underwound double-stranded DNA.
Underwinding gives rise to negative supercoils;
overwinding produces positive supercoils.
supersecondary structure. See motif.
Svedberg unit (S). A unit of 10 - 13 second
used for expressing the sedimentation coefficient, a measure of the rate at which a large
molecule or particle sediments in an ultracentrifuge. Large S values usually indicate
symport. The cotransport of two different
species of ions or molecules in the same direction across a membrane by a transport protein.
synonymous codons. Different codons that
specify the same amino acid.
synthase. A common name for an enzyme,
often a transferase, that catalyzes a synthetic
synthetase. An enzyme that catalyzes the joining of two substrates and requires the input of
the chemical potential energy of a nucleoside
triphosphate. Synthetases are members of the
IUBMB class of enzymes known as ligases.
T state. The less active conformation of an
allosteric protein; opposite of R state.
TATA box. An A/T-rich DNA sequence
found within the promoter of both prokaryotic and eukaryotic genes.
template strand. The strand of DNA within
a gene whose nucleotide sequence is complementary to that of the transcribed RNA. During transcription, RNA polymerase binds to
and moves along the template strand in the
3¿ : 5¿ direction, catalyzing the synthesis of
RNA in the 5¿ : 3¿ direction.
termination codon. A codon that is recognized by specific proteins that cause newly
synthesized peptides to be released from the
translation machinery thus terminating
translation. The three termination codons
(UAG, UAA, and UGA) are also known as
termination sequence. A sequence at the 3 ¿
end of a gene that mediates transcription
tertiary structure. The compacting of polymeric chains into one or more domains within a macromolecule. In proteins, tertiary
structure is stabilized mainly by hydrophobic
interactions between side chains.
thermodynamics. The branch of physical
science that studies transformations of heat
30 nm fiber. A chromatin structure in which
nucleosomes are coiled into a solenoid 30 nm
؊35 region. A sequence found within the
promoter of some prokaryotic genes about
30 to 35 base pairs upstream of the transcription initiation site.
GLOSSARY OF BIOCHEMICAL TERMS
310 helix. A secondary structure of proteins,
consisting of a helix in which the carbonyl
oxygen of each amino acid residue (residue
n) forms a hydrogen bond with the amide hydrogen of the third residue further toward
the C-terminus of the polypeptide chain
(residue n + 3).
thylakoid lamella. See thylakoid membrane.
thylakoid membrane. A highly folded, continuous membrane network suspended in
the aqueous matrix of the chloroplast. The
thylakoid membrane is the site of the lightdependent reactions of photosynthesis,
which lead to the formation of NADPH and
ATP. Also known as the thylakoid lamella.
Tm. See melting point and phase-transition
topoisomerase. An enzyme that alters the
supercoiling of a DNA molecule by cleaving a
phosphodiester linkage in either one or both
strands, rewinding the DNA, and resealing
the break. Some topoisomerases are also
known as DNA gyrases.
topology. 1. The arrangement of membranespanning segments and connecting loops in
an integral membrane protein. 2. The overall
morphology of a nucleic acid molecule.
TCC arm. The stem-and-loop structure in a
tRNA molecule that contains the sequence
trace element. An element required in very
small quantities by living organisms. Examples include copper, iron, and zinc.
transaminase. An enzyme that catalyzes the
transfer of an amino group from an a-amino
acid to an a-keto acid. Transaminases require
the coenzyme pyridoxal phosphate. They are
also called aminotransferases.
transcription. The copying of biological information from a double-stranded DNA
molecule to a single-stranded RNA molecule,
catalyzed by a transcription complex consisting of RNA polymerase and associated
transcription bubble. A short region of
double-stranded DNA that is unwound by
RNA polymerase during transcription.
transcription factor. A protein that binds to
the promoter region, to RNA polymerase, or
to both during assembly of the transcription
initiation complex. Some transcription
factors remain bound during RNA chain
transcription initiation complex. The complex of RNA polymerase and other factors
that assembles at the promoter at the start of
transcriptional activator. A regulatory DNAbinding protein that enhances the rate of
transcription by increasing the activity of
RNA polymerase at specific promoters.
transducer. The component of a signaltransduction pathway that couples receptorligand binding with generation of a second
messenger catalyzed by an effector enzyme.
transfer ribonucleic acid. See tRNA.
transferase. An enzyme that catalyzes a
group-transfer reaction. Transferases often
require a coenzyme.
transition state. An unstable, high-energy
arrangement of atoms in which chemical
bonds are being formed or broken. Transition states have structures between those of
the substrates and the products of a reaction.
transition-state analog. A compound that
resembles a transition state. Transition-state
analogs characteristically bind extremely
tightly to the active sites of appropriate enzymes and thus act as potent inhibitors.
transition-state stabilization. The increased
binding of transition states to enzymes relative
to the binding of substrates or products. Transition-state stabilization lowers the activation
energy and thus contributes to catalysis.
translation. The synthesis of a polypeptide
whose sequence reflects the nucleotide sequence of an mRNA molecule. Amino acids
are donated by activated tRNA molecules,
and peptide bond synthesis is catalyzed by
the translation complex, which includes the
ribosome and other factors.
translation complex. The complex of a ribosome and protein factors that carries out
the translation of mRNA in vivo.
translation initiation complex. The complex
of ribosomal subunits, an mRNA template, an
initiator tRNA molecule, and initiation factors
that assembles at the start of protein synthesis.
translation initiation factor. A protein involved in the formation of the initiation
complex at the start of protein synthesis.
translocation. 1. The movement of the ribosome by one codon along an mRNA molecule. 2. The movement of a polypeptide
through a membrane.
transposon. A mobile genetic element that
jumps between chromosomes or parts of a
chromosome by taking advantage of recombination mechanisms. Also known as a transposable element.
transverse diffusion. The passage of lipid or
protein molecules from one leaflet of a lipid
bilayer to the other leaflet. Unlike lateral diffusion within one leaflet of a bilayer, transverse diffusion is extremely slow.
triacylglycerol. A lipid containing three
fatty acyl residues esterified to glycerol. Fats
and oils are mixtures of triacylglycerols. Formerly known as a triglyceride.
tricarboxylic acid cycle. See citric acid cycle.
triglyceride. See triacylglycerol.
triose. A three-carbon sugar.
tRNA. A class of RNA molecules that carry
activated amino acids to the site of protein
synthesis for incorporation into growing
peptide chains. tRNA molecules contain an
anticodon that recognizes a complementary
codon in mRNA.
turn (in proteins). A protein loop of 4-5
residues that causes a change in the direction
of a polypeptide chain in a folded protein.
turnover. The dynamic metabolic steady
state in which molecules are degraded and replaced by newly synthesized molecules.
turnover number. See catalytic constant.
twist. The angle of rotation between adjacent residues within a helical macromolecule.
type I reaction center. The special pair of
chlorophyll molecules and associated electron transfer chain found in photosystem I.
type II reaction center. The reaction center
found in photosystem II.
uncompetitive inhibition. Inhibition of an
enzyme-catalyzed reaction by a reversible inhibitor that binds only to the enzyme-substrate complex, not to the free enzyme.
uncouplers. See uncoupling agent.
uncoupling agent. A compound that disrupts the usual tight coupling between electron transport and phosphorylation of ADP.
uniport. The transport of a single type of
solute across a membrane by a transport
unsaturated fatty acid. A fatty acid with at
least one carbon-carbon double bond. An unsaturated fatty acid with only one carbon-carbon double bond is called a monounsaturated
fatty acid. A fatty acid with two or more carbon-carbon double bonds is called a polyunsaturated fatty acid. In general, the double
bonds of unsaturated fatty acids are of the cis
configuration and are separated from each
other by methylene ( ¬ CH2 ¬ ) groups.
urea cycle. A metabolic cycle consisting of
four enzyme-catalyzed reactions that converts nitrogen from ammonia and aspartate
to urea. Four ATP equivalents are consumed
during formation of one molecule of urea.
v. See velocity.
v0. See initial velocity.
vacuole. A fluid-filled organelle in plant
cells that is a storage site for water, ions, or
van der Waals force. A weak intermolecular
force produced between neutral atoms by
transient electrostatic interactions. Van der
Waals attraction is strongest when atoms are
separated by the sum of their van der Waals
radii; strong van der Waals repulsion precludes closer approach.
van der Waals radius. The effective size of
an atom. The distance between the nuclei of
two nonbonded atoms at the point of maximal attraction is the sum of their van der
variable arm. The arm of a tRNA molecule
that is located between the anticodon arm
and the TcC arm. The variable arm can range
in length from about 3 to 21 nucleotides.
velocity (V). The rate of a chemical reaction,
expressed as amount of product formed per
very low density lipoprotein (VLDL). A
type of plasma lipoprotein that transports
endogenous triacylglycerols, cholesterol, and
cholesteryl esters from the liver to the tissues.